In applications manager when you add a new application or database for monitoring, the server in which that application is present will be also automatically added for monitoring. Once the server is added, applications manager will automatically try to discover the other applications ( Apache, IIS, Tomcat, JBoss, WebSphere, DB2, MSSQL, MySQL, Oracle, SNMP and JMX application ) which are running in their corresponding default ports.
These automatically discovered servers and applications will be also taken for licensing count. If you do not want the automatically discovered applications, you can either delete them or unmanage them ( unmanaged monitors will not be taken for licensing count ). But if you delete the automatically discovered server, all the applications under that server will be also deleted. So unmanaging the server is a recommended option.